Starting phenix.real_space_refine on Fri Jan 17 11:53:05 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/9b3p_44148/01_2025/9b3p_44148.cif Found real_map, /net/cci-nas-00/data/ceres_data/9b3p_44148/01_2025/9b3p_44148.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.0 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/cci-nas-00/data/ceres_data/9b3p_44148/01_2025/9b3p_44148.map" default_real_map = "/net/cci-nas-00/data/ceres_data/9b3p_44148/01_2025/9b3p_44148.map" model { file = "/net/cci-nas-00/data/ceres_data/9b3p_44148/01_2025/9b3p_44148.cif" } default_model = "/net/cci-nas-00/data/ceres_data/9b3p_44148/01_2025/9b3p_44148.cif" } resolution = 3.0 write_initial_geo_file = False refinement { macro_cycles = 10 } qi { qm_restraints { package { program = *test } } } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= 0.000 sd= 0.004 Set stop_for_unknowns flag Set to: True Assert model is a single copy model Assert all atoms have isotropic ADPs Construct map_model_manager Extract box with map and model Check model and map are aligned Set scattering table Set to: electron Number of scattering types: 5 Type Number sf(0) Gaussians P 256 5.49 5 S 10 5.16 5 C 6151 2.51 5 N 2078 2.21 5 O 2572 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 11 residue(s): 0.02s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5571/modules/chem_data/mon_lib" Total number of atoms: 11067 Number of models: 1 Model: "" Number of chains: 10 Chain: "A" Number of atoms: 797 Number of conformers: 1 Conformer: "" Number of residues, atoms: 97, 797 Classifications: {'peptide': 97} Link IDs: {'PTRANS': 3, 'TRANS': 93} Chain: "B" Number of atoms: 619 Number of conformers: 1 Conformer: "" Number of residues, atoms: 78, 619 Classifications: {'peptide': 78} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 1, 'TRANS': 76} Chain: "C" Number of atoms: 740 Number of conformers: 1 Conformer: "" Number of residues, atoms: 98, 740 Classifications: {'peptide': 98} Link IDs: {'CIS': 1, 'PTRANS': 3, 'TRANS': 93} Chain: "D" Number of atoms: 719 Number of conformers: 1 Conformer: "" Number of residues, atoms: 92, 719 Classifications: {'peptide': 92} Link IDs: {'PTRANS': 2, 'TRANS': 89} Chain: "E" Number of atoms: 803 Number of conformers: 1 Conformer: "" Number of residues, atoms: 98, 803 Classifications: {'peptide': 98} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 3, 'TRANS': 94} Chain: "F" Number of atoms: 646 Number of conformers: 1 Conformer: "" Number of residues, atoms: 81, 646 Classifications: {'peptide': 81} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 1, 'TRANS': 79} Chain: "G" Number of atoms: 776 Number of conformers: 1 Conformer: "" Number of residues, atoms: 102, 776 Classifications: {'peptide': 102} Link IDs: {'CIS': 1, 'PTRANS': 3, 'TRANS': 97} Chain: "H" Number of atoms: 719 Number of conformers: 1 Conformer: "" Number of residues, atoms: 92, 719 Classifications: {'peptide': 92} Link IDs: {'PTRANS': 2, 'TRANS': 89} Chain: "I" Number of atoms: 2639 Number of conformers: 1 Conformer: "" Number of residues, atoms: 128, 2639 Classifications: {'DNA': 128} Link IDs: {'rna3p': 127} Chain: "J" Number of atoms: 2609 Number of conformers: 1 Conformer: "" Number of residues, atoms: 128, 2609 Classifications: {'DNA': 128} Link IDs: {'rna3p': 127} Time building chain proxies: 6.55, per 1000 atoms: 0.59 Number of scatterers: 11067 At special positions: 0 Unit cell: (103.68, 115.56, 117.72, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 5 Type Number sf(0) S 10 16.00 P 256 15.00 O 2572 8.00 N 2078 7.00 C 6151 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=0, symmetry=0 Automatic linking Parameters for automatic linking Linking & cutoffs Metal : Auto - 3.00 Amino acid : True - 1.90 Carbohydrate : True - 1.99 Ligands : True - 1.99 Small molecules : False - 1.98 Amino acid - RNA/DNA : False Number of custom bonds: simple=0, symmetry=0 Time building additional restraints: 2.78 Conformation dependent library (CDL) restraints added in 808.3 milliseconds 1444 Ramachandran restraints generated. 722 Oldfield, 0 Emsley, 722 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 1372 Finding SS restraints... Secondary structure from input PDB file: 34 helices and 4 sheets defined 69.4% alpha, 1.1% beta 12 base pairs and 159 stacking pairs defined. Time for finding SS restraints: 3.57 Creating SS restraints... Processing helix chain 'A' and resid 44 through 50 removed outlier: 3.704A pdb=" N GLU A 50 " --> pdb=" O VAL A 46 " (cutoff:3.500A) Processing helix chain 'A' and resid 50 through 55 Processing helix chain 'A' and resid 64 through 79 removed outlier: 3.507A pdb=" N ARG A 69 " --> pdb=" O LEU A 65 " (cutoff:3.500A) removed outlier: 3.609A pdb=" N LEU A 70 " --> pdb=" O PRO A 66 " (cutoff:3.500A) removed outlier: 3.941A pdb=" N ASP A 77 " --> pdb=" O GLU A 73 " (cutoff:3.500A) removed outlier: 4.084A pdb=" N PHE A 78 " --> pdb=" O ILE A 74 " (cutoff:3.500A) Processing helix chain 'A' and resid 85 through 114 removed outlier: 3.731A pdb=" N ILE A 89 " --> pdb=" O GLN A 85 " (cutoff:3.500A) removed outlier: 4.019A pdb=" N GLY A 90 " --> pdb=" O SER A 86 " (cutoff:3.500A) removed outlier: 3.820A pdb=" N ASP A 106 " --> pdb=" O GLY A 102 " (cutoff:3.500A) removed outlier: 3.539A pdb=" N LEU A 109 " --> pdb=" O GLU A 105 " (cutoff:3.500A) removed outlier: 3.665A pdb=" N CYS A 110 " --> pdb=" O ASP A 106 " (cutoff:3.500A) removed outlier: 3.730A pdb=" N ALA A 111 " --> pdb=" O THR A 107 " (cutoff:3.500A) Processing helix chain 'A' and resid 121 through 132 removed outlier: 4.164A pdb=" N GLN A 125 " --> pdb=" O PRO A 121 " (cutoff:3.500A) removed outlier: 3.527A pdb=" N LEU A 126 " --> pdb=" O LYS A 122 " (cutoff:3.500A) removed outlier: 3.619A pdb=" N ILE A 130 " --> pdb=" O LEU A 126 " (cutoff:3.500A) Processing helix chain 'B' and resid 30 through 42 removed outlier: 3.681A pdb=" N ILE B 34 " --> pdb=" O THR B 30 " (cutoff:3.500A) removed outlier: 3.520A pdb=" N LEU B 37 " --> pdb=" O ALA B 33 " (cutoff:3.500A) removed outlier: 3.928A pdb=" N ARG B 40 " --> pdb=" O ARG B 36 " (cutoff:3.500A) removed outlier: 3.989A pdb=" N GLY B 41 " --> pdb=" O LEU B 37 " (cutoff:3.500A) Processing helix chain 'B' and resid 49 through 75 removed outlier: 3.772A pdb=" N ARG B 55 " --> pdb=" O TYR B 51 " (cutoff:3.500A) removed outlier: 4.209A pdb=" N GLY B 56 " --> pdb=" O GLU B 52 " (cutoff:3.500A) removed outlier: 3.701A pdb=" N ASN B 64 " --> pdb=" O VAL B 60 " (cutoff:3.500A) removed outlier: 3.776A pdb=" N VAL B 65 " --> pdb=" O PHE B 61 " (cutoff:3.500A) removed outlier: 3.515A pdb=" N ARG B 67 " --> pdb=" O GLU B 63 " (cutoff:3.500A) removed outlier: 3.502A pdb=" N ASP B 68 " --> pdb=" O ASN B 64 " (cutoff:3.500A) Processing helix chain 'B' and resid 83 through 94 removed outlier: 3.967A pdb=" N VAL B 87 " --> pdb=" O ALA B 83 " (cutoff:3.500A) removed outlier: 4.173A pdb=" N ARG B 92 " --> pdb=" O TYR B 88 " (cutoff:3.500A) removed outlier: 4.005A pdb=" N GLN B 93 " --> pdb=" O ALA B 89 " (cutoff:3.500A) Processing helix chain 'C' and resid 18 through 24 removed outlier: 3.533A pdb=" N ARG C 22 " --> pdb=" O SER C 18 " (cutoff:3.500A) removed outlier: 3.567A pdb=" N ALA C 23 " --> pdb=" O ARG C 19 " (cutoff:3.500A) Processing helix chain 'C' and resid 28 through 40 removed outlier: 3.709A pdb=" N ILE C 32 " --> pdb=" O PRO C 28 " (cutoff:3.500A) removed outlier: 3.783A pdb=" N LYS C 37 " --> pdb=" O HIS C 33 " (cutoff:3.500A) removed outlier: 3.963A pdb=" N SER C 38 " --> pdb=" O ARG C 34 " (cutoff:3.500A) removed outlier: 3.658A pdb=" N ARG C 39 " --> pdb=" O HIS C 35 " (cutoff:3.500A) removed outlier: 3.534A pdb=" N THR C 40 " --> pdb=" O LEU C 36 " (cutoff:3.500A) Processing helix chain 'C' and resid 47 through 74 removed outlier: 3.887A pdb=" N ALA C 51 " --> pdb=" O GLY C 47 " (cutoff:3.500A) removed outlier: 3.918A pdb=" N VAL C 52 " --> pdb=" O ALA C 48 " (cutoff:3.500A) removed outlier: 3.545A pdb=" N ALA C 56 " --> pdb=" O VAL C 52 " (cutoff:3.500A) removed outlier: 3.666A pdb=" N LEU C 68 " --> pdb=" O GLU C 64 " (cutoff:3.500A) removed outlier: 3.553A pdb=" N ALA C 72 " --> pdb=" O LEU C 68 " (cutoff:3.500A) Processing helix chain 'C' and resid 82 through 92 removed outlier: 3.585A pdb=" N LEU C 86 " --> pdb=" O THR C 82 " (cutoff:3.500A) removed outlier: 3.635A pdb=" N GLN C 87 " --> pdb=" O PRO C 83 " (cutoff:3.500A) removed outlier: 3.513A pdb=" N LEU C 88 " --> pdb=" O ARG C 84 " (cutoff:3.500A) removed outlier: 3.543A pdb=" N ILE C 90 " --> pdb=" O LEU C 86 " (cutoff:3.500A) Processing helix chain 'C' and resid 94 through 100 removed outlier: 3.771A pdb=" N SER C 98 " --> pdb=" O GLU C 94 " (cutoff:3.500A) removed outlier: 3.948A pdb=" N LEU C 99 " --> pdb=" O GLU C 95 " (cutoff:3.500A) removed outlier: 3.507A pdb=" N ILE C 100 " --> pdb=" O LEU C 96 " (cutoff:3.500A) No H-bonds generated for 'chain 'C' and resid 94 through 100' Processing helix chain 'D' and resid 40 through 49 removed outlier: 3.651A pdb=" N VAL D 44 " --> pdb=" O TYR D 40 " (cutoff:3.500A) removed outlier: 3.712A pdb=" N GLN D 47 " --> pdb=" O LYS D 43 " (cutoff:3.500A) removed outlier: 3.652A pdb=" N VAL D 48 " --> pdb=" O VAL D 44 " (cutoff:3.500A) Processing helix chain 'D' and resid 55 through 83 removed outlier: 3.564A pdb=" N SER D 60 " --> pdb=" O SER D 56 " (cutoff:3.500A) removed outlier: 3.917A pdb=" N ILE D 61 " --> pdb=" O LYS D 57 " (cutoff:3.500A) removed outlier: 3.901A pdb=" N ARG D 79 " --> pdb=" O GLY D 75 " (cutoff:3.500A) removed outlier: 3.614A pdb=" N LEU D 80 " --> pdb=" O GLU D 76 " (cutoff:3.500A) removed outlier: 3.838A pdb=" N ALA D 81 " --> pdb=" O ALA D 77 " (cutoff:3.500A) removed outlier: 3.528A pdb=" N HIS D 82 " --> pdb=" O SER D 78 " (cutoff:3.500A) Processing helix chain 'D' and resid 90 through 102 removed outlier: 3.886A pdb=" N ILE D 94 " --> pdb=" O THR D 90 " (cutoff:3.500A) removed outlier: 3.907A pdb=" N ARG D 99 " --> pdb=" O GLN D 95 " (cutoff:3.500A) removed outlier: 3.679A pdb=" N LEU D 100 " --> pdb=" O THR D 96 " (cutoff:3.500A) Processing helix chain 'D' and resid 105 through 123 removed outlier: 3.801A pdb=" N HIS D 109 " --> pdb=" O GLU D 105 " (cutoff:3.500A) removed outlier: 3.745A pdb=" N VAL D 111 " --> pdb=" O ALA D 107 " (cutoff:3.500A) removed outlier: 3.898A pdb=" N SER D 112 " --> pdb=" O LYS D 108 " (cutoff:3.500A) removed outlier: 3.572A pdb=" N LYS D 116 " --> pdb=" O SER D 112 " (cutoff:3.500A) removed outlier: 4.088A pdb=" N ALA D 117 " --> pdb=" O GLU D 113 " (cutoff:3.500A) removed outlier: 3.585A pdb=" N VAL D 118 " --> pdb=" O GLY D 114 " (cutoff:3.500A) Processing helix chain 'E' and resid 50 through 55 removed outlier: 3.573A pdb=" N GLN E 55 " --> pdb=" O ILE E 51 " (cutoff:3.500A) Processing helix chain 'E' and resid 64 through 79 removed outlier: 3.637A pdb=" N ARG E 69 " --> pdb=" O LEU E 65 " (cutoff:3.500A) removed outlier: 3.605A pdb=" N LEU E 70 " --> pdb=" O PRO E 66 " (cutoff:3.500A) removed outlier: 4.290A pdb=" N ASP E 77 " --> pdb=" O GLU E 73 " (cutoff:3.500A) removed outlier: 4.283A pdb=" N PHE E 78 " --> pdb=" O ILE E 74 " (cutoff:3.500A) removed outlier: 3.645A pdb=" N LYS E 79 " --> pdb=" O ALA E 75 " (cutoff:3.500A) Processing helix chain 'E' and resid 85 through 114 removed outlier: 3.582A pdb=" N ILE E 89 " --> pdb=" O GLN E 85 " (cutoff:3.500A) removed outlier: 3.966A pdb=" N GLY E 90 " --> pdb=" O SER E 86 " (cutoff:3.500A) removed outlier: 3.510A pdb=" N LEU E 92 " --> pdb=" O ALA E 88 " (cutoff:3.500A) removed outlier: 3.630A pdb=" N ASP E 106 " --> pdb=" O GLY E 102 " (cutoff:3.500A) removed outlier: 3.504A pdb=" N LEU E 109 " --> pdb=" O GLU E 105 " (cutoff:3.500A) removed outlier: 3.734A pdb=" N CYS E 110 " --> pdb=" O ASP E 106 " (cutoff:3.500A) removed outlier: 3.844A pdb=" N ALA E 111 " --> pdb=" O THR E 107 " (cutoff:3.500A) removed outlier: 3.735A pdb=" N ILE E 112 " --> pdb=" O ASN E 108 " (cutoff:3.500A) Processing helix chain 'E' and resid 120 through 132 removed outlier: 3.806A pdb=" N ILE E 124 " --> pdb=" O MET E 120 " (cutoff:3.500A) removed outlier: 3.932A pdb=" N GLN E 125 " --> pdb=" O PRO E 121 " (cutoff:3.500A) removed outlier: 3.836A pdb=" N LEU E 126 " --> pdb=" O LYS E 122 " (cutoff:3.500A) removed outlier: 3.661A pdb=" N ALA E 127 " --> pdb=" O ASP E 123 " (cutoff:3.500A) removed outlier: 3.818A pdb=" N ILE E 130 " --> pdb=" O LEU E 126 " (cutoff:3.500A) removed outlier: 3.543A pdb=" N ARG E 131 " --> pdb=" O ALA E 127 " (cutoff:3.500A) Processing helix chain 'F' and resid 24 through 29 removed outlier: 4.255A pdb=" N GLN F 27 " --> pdb=" O ASP F 24 " (cutoff:3.500A) removed outlier: 3.559A pdb=" N GLY F 28 " --> pdb=" O ASN F 25 " (cutoff:3.500A) removed outlier: 4.263A pdb=" N ILE F 29 " --> pdb=" O ILE F 26 " (cutoff:3.500A) No H-bonds generated for 'chain 'F' and resid 24 through 29' Processing helix chain 'F' and resid 30 through 39 removed outlier: 3.708A pdb=" N ILE F 34 " --> pdb=" O THR F 30 " (cutoff:3.500A) removed outlier: 3.776A pdb=" N LEU F 37 " --> pdb=" O ALA F 33 " (cutoff:3.500A) Processing helix chain 'F' and resid 49 through 75 removed outlier: 3.666A pdb=" N ARG F 55 " --> pdb=" O TYR F 51 " (cutoff:3.500A) removed outlier: 4.299A pdb=" N GLY F 56 " --> pdb=" O GLU F 52 " (cutoff:3.500A) removed outlier: 3.804A pdb=" N ASN F 64 " --> pdb=" O VAL F 60 " (cutoff:3.500A) removed outlier: 3.829A pdb=" N VAL F 65 " --> pdb=" O PHE F 61 " (cutoff:3.500A) removed outlier: 3.723A pdb=" N ARG F 67 " --> pdb=" O GLU F 63 " (cutoff:3.500A) removed outlier: 3.513A pdb=" N THR F 71 " --> pdb=" O ARG F 67 " (cutoff:3.500A) Processing helix chain 'F' and resid 83 through 94 removed outlier: 3.817A pdb=" N VAL F 87 " --> pdb=" O ALA F 83 " (cutoff:3.500A) removed outlier: 3.972A pdb=" N ARG F 92 " --> pdb=" O TYR F 88 " (cutoff:3.500A) removed outlier: 3.821A pdb=" N GLN F 93 " --> pdb=" O ALA F 89 " (cutoff:3.500A) removed outlier: 3.531A pdb=" N GLY F 94 " --> pdb=" O LEU F 90 " (cutoff:3.500A) Processing helix chain 'G' and resid 18 through 24 removed outlier: 3.648A pdb=" N ARG G 22 " --> pdb=" O SER G 18 " (cutoff:3.500A) removed outlier: 3.675A pdb=" N ALA G 23 " --> pdb=" O ARG G 19 " (cutoff:3.500A) Processing helix chain 'G' and resid 28 through 37 removed outlier: 3.672A pdb=" N ILE G 32 " --> pdb=" O PRO G 28 " (cutoff:3.500A) removed outlier: 3.625A pdb=" N LYS G 37 " --> pdb=" O HIS G 33 " (cutoff:3.500A) Processing helix chain 'G' and resid 47 through 73 removed outlier: 3.858A pdb=" N ALA G 51 " --> pdb=" O GLY G 47 " (cutoff:3.500A) removed outlier: 3.738A pdb=" N VAL G 52 " --> pdb=" O ALA G 48 " (cutoff:3.500A) removed outlier: 3.686A pdb=" N TYR G 53 " --> pdb=" O THR G 49 " (cutoff:3.500A) removed outlier: 3.569A pdb=" N ALA G 56 " --> pdb=" O VAL G 52 " (cutoff:3.500A) removed outlier: 3.548A pdb=" N ILE G 57 " --> pdb=" O TYR G 53 " (cutoff:3.500A) removed outlier: 3.595A pdb=" N LEU G 58 " --> pdb=" O SER G 54 " (cutoff:3.500A) removed outlier: 3.554A pdb=" N VAL G 65 " --> pdb=" O LEU G 61 " (cutoff:3.500A) removed outlier: 3.542A pdb=" N LEU G 68 " --> pdb=" O GLU G 64 " (cutoff:3.500A) removed outlier: 3.920A pdb=" N ALA G 72 " --> pdb=" O LEU G 68 " (cutoff:3.500A) removed outlier: 3.608A pdb=" N SER G 73 " --> pdb=" O ALA G 69 " (cutoff:3.500A) Processing helix chain 'G' and resid 82 through 92 removed outlier: 3.533A pdb=" N LEU G 86 " --> pdb=" O THR G 82 " (cutoff:3.500A) removed outlier: 3.557A pdb=" N GLN G 87 " --> pdb=" O PRO G 83 " (cutoff:3.500A) Processing helix chain 'G' and resid 114 through 118 removed outlier: 3.550A pdb=" N LEU G 117 " --> pdb=" O HIS G 114 " (cutoff:3.500A) removed outlier: 3.921A pdb=" N ILE G 118 " --> pdb=" O LYS G 115 " (cutoff:3.500A) No H-bonds generated for 'chain 'G' and resid 114 through 118' Processing helix chain 'H' and resid 40 through 49 removed outlier: 3.659A pdb=" N VAL H 44 " --> pdb=" O TYR H 40 " (cutoff:3.500A) removed outlier: 3.622A pdb=" N GLN H 47 " --> pdb=" O LYS H 43 " (cutoff:3.500A) removed outlier: 3.531A pdb=" N VAL H 48 " --> pdb=" O VAL H 44 " (cutoff:3.500A) Processing helix chain 'H' and resid 55 through 84 removed outlier: 3.972A pdb=" N SER H 60 " --> pdb=" O SER H 56 " (cutoff:3.500A) removed outlier: 3.919A pdb=" N ILE H 61 " --> pdb=" O LYS H 57 " (cutoff:3.500A) removed outlier: 3.707A pdb=" N ARG H 79 " --> pdb=" O GLY H 75 " (cutoff:3.500A) removed outlier: 3.608A pdb=" N LEU H 80 " --> pdb=" O GLU H 76 " (cutoff:3.500A) removed outlier: 3.863A pdb=" N ALA H 81 " --> pdb=" O ALA H 77 " (cutoff:3.500A) removed outlier: 3.759A pdb=" N HIS H 82 " --> pdb=" O SER H 78 " (cutoff:3.500A) Processing helix chain 'H' and resid 90 through 102 removed outlier: 3.999A pdb=" N ILE H 94 " --> pdb=" O THR H 90 " (cutoff:3.500A) removed outlier: 3.506A pdb=" N ALA H 97 " --> pdb=" O GLU H 93 " (cutoff:3.500A) removed outlier: 3.536A pdb=" N VAL H 98 " --> pdb=" O ILE H 94 " (cutoff:3.500A) removed outlier: 3.826A pdb=" N ARG H 99 " --> pdb=" O GLN H 95 " (cutoff:3.500A) removed outlier: 3.647A pdb=" N LEU H 100 " --> pdb=" O THR H 96 " (cutoff:3.500A) Processing helix chain 'H' and resid 105 through 123 removed outlier: 3.998A pdb=" N HIS H 109 " --> pdb=" O GLU H 105 " (cutoff:3.500A) removed outlier: 3.769A pdb=" N VAL H 111 " --> pdb=" O ALA H 107 " (cutoff:3.500A) removed outlier: 3.852A pdb=" N SER H 112 " --> pdb=" O LYS H 108 " (cutoff:3.500A) removed outlier: 3.547A pdb=" N LYS H 116 " --> pdb=" O SER H 112 " (cutoff:3.500A) removed outlier: 4.268A pdb=" N ALA H 117 " --> pdb=" O GLU H 113 " (cutoff:3.500A) removed outlier: 3.646A pdb=" N VAL H 118 " --> pdb=" O GLY H 114 " (cutoff:3.500A) removed outlier: 3.540A pdb=" N LYS H 120 " --> pdb=" O LYS H 116 " (cutoff:3.500A) Processing sheet with id=AA1, first strand: chain 'A' and resid 83 through 84 removed outlier: 6.869A pdb=" N ARG A 83 " --> pdb=" O VAL B 81 " (cutoff:3.500A) No H-bonds generated for sheet with id=AA1 Processing sheet with id=AA2, first strand: chain 'C' and resid 45 through 46 removed outlier: 7.077A pdb=" N ARG C 45 " --> pdb=" O ILE D 89 " (cutoff:3.500A) No H-bonds generated for sheet with id=AA2 Processing sheet with id=AA3, first strand: chain 'E' and resid 83 through 84 removed outlier: 6.808A pdb=" N ARG E 83 " --> pdb=" O VAL F 81 " (cutoff:3.500A) No H-bonds generated for sheet with id=AA3 Processing sheet with id=AA4, first strand: chain 'G' and resid 45 through 46 removed outlier: 6.322A pdb=" N ARG G 45 " --> pdb=" O ILE H 89 " (cutoff:3.500A) No H-bonds generated for sheet with id=AA4 240 hydrogen bonds defined for protein. 720 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 29 hydrogen bonds 58 hydrogen bond angles 0 basepair planarities 12 basepair parallelities 159 stacking parallelities Total time for adding SS restraints: 3.02 Time building geometry restraints manager: 3.16 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.22 - 1.34: 2443 1.34 - 1.45: 3593 1.45 - 1.57: 5222 1.57 - 1.69: 510 1.69 - 1.81: 18 Bond restraints: 11786 Sorted by residual: bond pdb=" C3' DT I -32 " pdb=" O3' DT I -32 " ideal model delta sigma weight residual 1.422 1.455 -0.033 3.00e-02 1.11e+03 1.25e+00 bond pdb=" CA ILE F 29 " pdb=" CB ILE F 29 " ideal model delta sigma weight residual 1.530 1.539 -0.009 1.05e-02 9.07e+03 7.25e-01 bond pdb=" C3' DT I -50 " pdb=" O3' DT I -50 " ideal model delta sigma weight residual 1.422 1.447 -0.025 3.00e-02 1.11e+03 6.98e-01 bond pdb=" C3' DT I -59 " pdb=" O3' DT I -59 " ideal model delta sigma weight residual 1.422 1.446 -0.024 3.00e-02 1.11e+03 6.62e-01 bond pdb=" C THR H 90 " pdb=" O THR H 90 " ideal model delta sigma weight residual 1.244 1.236 0.008 1.17e-02 7.31e+03 4.90e-01 ... (remaining 11781 not shown) Histogram of bond angle deviations from ideal: 0.00 - 0.99: 16595 0.99 - 1.98: 272 1.98 - 2.97: 137 2.97 - 3.96: 2 3.96 - 4.95: 6 Bond angle restraints: 17012 Sorted by residual: angle pdb=" C THR H 90 " pdb=" CA THR H 90 " pdb=" CB THR H 90 " ideal model delta sigma weight residual 114.40 110.29 4.11 1.25e+00 6.40e-01 1.08e+01 angle pdb=" C LEU C 76 " pdb=" N LYS C 77 " pdb=" CA LYS C 77 " ideal model delta sigma weight residual 121.54 125.67 -4.13 1.91e+00 2.74e-01 4.67e+00 angle pdb=" C3' DT I -32 " pdb=" O3' DT I -32 " pdb=" P DA I -31 " ideal model delta sigma weight residual 120.20 122.92 -2.72 1.50e+00 4.44e-01 3.29e+00 angle pdb=" C7 DT I 15 " pdb=" C5 DT I 15 " pdb=" C6 DT I 15 " ideal model delta sigma weight residual 124.00 121.74 2.26 1.50e+00 4.44e-01 2.27e+00 angle pdb=" C7 DT J 1 " pdb=" C5 DT J 1 " pdb=" C6 DT J 1 " ideal model delta sigma weight residual 124.00 121.74 2.26 1.50e+00 4.44e-01 2.27e+00 ... (remaining 17007 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 34.64: 5475 34.64 - 69.28: 926 69.28 - 103.92: 7 103.92 - 138.55: 1 138.55 - 173.19: 2 Dihedral angle restraints: 6411 sinusoidal: 4281 harmonic: 2130 Sorted by residual: dihedral pdb=" C4' DT I -32 " pdb=" C3' DT I -32 " pdb=" O3' DT I -32 " pdb=" P DA I -31 " ideal model delta sinusoidal sigma weight residual -140.00 33.19 -173.19 1 3.50e+01 8.16e-04 1.56e+01 dihedral pdb=" C4' DT I -59 " pdb=" C3' DT I -59 " pdb=" O3' DT I -59 " pdb=" P DC I -58 " ideal model delta sinusoidal sigma weight residual 220.00 80.29 139.71 1 3.50e+01 8.16e-04 1.38e+01 dihedral pdb=" C4' DT I -50 " pdb=" C3' DT I -50 " pdb=" O3' DT I -50 " pdb=" P DG I -49 " ideal model delta sinusoidal sigma weight residual 220.00 84.81 135.19 1 3.50e+01 8.16e-04 1.34e+01 ... (remaining 6408 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.025: 1510 0.025 - 0.051: 300 0.051 - 0.076: 83 0.076 - 0.101: 30 0.101 - 0.127: 18 Chirality restraints: 1941 Sorted by residual: chirality pdb=" CA ILE H 54 " pdb=" N ILE H 54 " pdb=" C ILE H 54 " pdb=" CB ILE H 54 " both_signs ideal model delta sigma weight residual False 2.43 2.56 -0.13 2.00e-01 2.50e+01 4.02e-01 chirality pdb=" CA ILE C 110 " pdb=" N ILE C 110 " pdb=" C ILE C 110 " pdb=" CB ILE C 110 " both_signs ideal model delta sigma weight residual False 2.43 2.55 -0.12 2.00e-01 2.50e+01 3.44e-01 chirality pdb=" CA ILE G 110 " pdb=" N ILE G 110 " pdb=" C ILE G 110 " pdb=" CB ILE G 110 " both_signs ideal model delta sigma weight residual False 2.43 2.55 -0.12 2.00e-01 2.50e+01 3.38e-01 ... (remaining 1938 not shown) Planarity restraints: 1262 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C THR G 82 " -0.013 5.00e-02 4.00e+02 1.93e-02 5.99e-01 pdb=" N PRO G 83 " 0.033 5.00e-02 4.00e+02 pdb=" CA PRO G 83 " -0.010 5.00e-02 4.00e+02 pdb=" CD PRO G 83 " -0.011 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C THR C 82 " -0.012 5.00e-02 4.00e+02 1.82e-02 5.29e-01 pdb=" N PRO C 83 " 0.031 5.00e-02 4.00e+02 pdb=" CA PRO C 83 " -0.009 5.00e-02 4.00e+02 pdb=" CD PRO C 83 " -0.010 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C MET A 120 " 0.012 5.00e-02 4.00e+02 1.75e-02 4.88e-01 pdb=" N PRO A 121 " -0.030 5.00e-02 4.00e+02 pdb=" CA PRO A 121 " 0.009 5.00e-02 4.00e+02 pdb=" CD PRO A 121 " 0.010 5.00e-02 4.00e+02 ... (remaining 1259 not shown) Histogram of nonbonded interaction distances: 2.29 - 2.81: 2628 2.81 - 3.34: 8621 3.34 - 3.86: 18528 3.86 - 4.38: 22781 4.38 - 4.90: 33678 Nonbonded interactions: 86236 Sorted by model distance: nonbonded pdb=" OG1 THR C 41 " pdb=" N SER C 42 " model vdw 2.292 3.120 nonbonded pdb=" OG1 THR G 41 " pdb=" N SER G 42 " model vdw 2.311 3.120 nonbonded pdb=" OH TYR D 40 " pdb=" OP1 DG I 48 " model vdw 2.337 3.040 nonbonded pdb=" NE2 HIS A 113 " pdb=" OD1 ASP E 123 " model vdw 2.376 3.120 nonbonded pdb=" O HIS G 43 " pdb=" OG SER H 87 " model vdw 2.377 3.040 ... (remaining 86231 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model Time spend for trying shortcut: 0.00 Found NCS groups: ncs_group { reference = chain 'A' selection = (chain 'E' and resid 38 through 134) } ncs_group { reference = chain 'B' selection = (chain 'F' and resid 25 through 102) } ncs_group { reference = (chain 'C' and resid 17 through 113) selection = (chain 'G' and resid 17 through 113) } ncs_group { reference = chain 'D' selection = chain 'H' } Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=1.00 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as individual isotropic Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 0.950 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.010 Extract box with map and model: 0.390 Check model and map are aligned: 0.080 Set scattering table: 0.090 Process input model: 27.510 Find NCS groups from input model: 0.270 Set up NCS constraints: 0.050 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.010 Load rotamer database and sin/cos tables:11.870 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 41.230 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6683 moved from start: 0.0000 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.033 11786 Z= 0.102 Angle : 0.374 4.949 17012 Z= 0.250 Chirality : 0.027 0.127 1941 Planarity : 0.002 0.019 1262 Dihedral : 24.092 173.192 5039 Min Nonbonded Distance : 2.292 Molprobity Statistics. All-atom Clashscore : 3.54 Ramachandran Plot: Outliers : 0.55 % Allowed : 4.57 % Favored : 94.88 % Rotamer: Outliers : 0.16 % Allowed : 4.93 % Favored : 94.90 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.28 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -5.86 (0.18), residues: 722 helix: -4.69 (0.06), residues: 424 sheet: None (None), residues: 0 loop : -2.32 (0.27), residues: 298 Max deviation from planes: Type MaxDev MeanDev LineInFile HIS 0.001 0.000 HIS D 82 PHE 0.001 0.000 PHE F 100 TYR 0.001 0.000 TYR F 72 ARG 0.001 0.000 ARG G 91 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1444 Ramachandran restraints generated. 722 Oldfield, 0 Emsley, 722 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1444 Ramachandran restraints generated. 722 Oldfield, 0 Emsley, 722 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 154 residues out of total 608 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 153 time to evaluate : 0.901 Fit side-chains REVERT: G 64 GLU cc_start: 0.7722 (tp30) cc_final: 0.7507 (mm-30) REVERT: G 87 GLN cc_start: 0.8141 (tp40) cc_final: 0.7869 (tp40) outliers start: 1 outliers final: 1 residues processed: 154 average time/residue: 1.7163 time to fit residues: 279.4447 Evaluate side-chains 93 residues out of total 608 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 92 time to evaluate : 0.798 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain H residue 59 MET Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 94 random chunks: chunk 79 optimal weight: 3.9990 chunk 71 optimal weight: 4.9990 chunk 39 optimal weight: 0.7980 chunk 24 optimal weight: 0.6980 chunk 48 optimal weight: 0.0570 chunk 38 optimal weight: 0.6980 chunk 73 optimal weight: 3.9990 chunk 28 optimal weight: 1.9990 chunk 44 optimal weight: 0.5980 chunk 54 optimal weight: 0.7980 chunk 85 optimal weight: 3.9990 overall best weight: 0.5698 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 25 ASN D 63 ASN ** E 68 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** F 25 ASN G 26 GLN H 63 ASN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4099 r_free = 0.4099 target = 0.183151 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 53)----------------| | r_work = 0.3758 r_free = 0.3758 target = 0.151434 restraints weight = 13920.079| |-----------------------------------------------------------------------------| r_work (start): 0.3741 rms_B_bonded: 0.82 r_work: 0.3606 rms_B_bonded: 2.50 restraints_weight: 0.5000 r_work: 0.3493 rms_B_bonded: 4.20 restraints_weight: 0.2500 r_work (final): 0.3493 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7715 moved from start: 0.3131 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.128 11786 Z= 0.226 Angle : 0.544 11.606 17012 Z= 0.310 Chirality : 0.033 0.129 1941 Planarity : 0.004 0.033 1262 Dihedral : 27.622 170.130 3621 Min Nonbonded Distance : 2.496 Molprobity Statistics. All-atom Clashscore : 3.84 Ramachandran Plot: Outliers : 0.28 % Allowed : 1.94 % Favored : 97.78 % Rotamer: Outliers : 2.63 % Allowed : 14.80 % Favored : 82.57 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.28 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -2.96 (0.24), residues: 722 helix: -1.66 (0.19), residues: 474 sheet: None (None), residues: 0 loop : -2.29 (0.30), residues: 248 Max deviation from planes: Type MaxDev MeanDev LineInFile HIS 0.006 0.001 HIS A 113 PHE 0.011 0.001 PHE F 61 TYR 0.015 0.002 TYR C 53 ARG 0.005 0.000 ARG G 34 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1444 Ramachandran restraints generated. 722 Oldfield, 0 Emsley, 722 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1444 Ramachandran restraints generated. 722 Oldfield, 0 Emsley, 722 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 137 residues out of total 608 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 16 poor density : 121 time to evaluate : 0.839 Fit side-chains REVERT: E 48 LEU cc_start: 0.8572 (mt) cc_final: 0.8176 (mp) REVERT: F 95 ARG cc_start: 0.7794 (OUTLIER) cc_final: 0.7541 (mtt180) REVERT: H 93 GLU cc_start: 0.8168 (OUTLIER) cc_final: 0.7498 (mp0) outliers start: 16 outliers final: 5 residues processed: 133 average time/residue: 1.8785 time to fit residues: 262.7478 Evaluate side-chains 110 residues out of total 608 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 7 poor density : 103 time to evaluate : 0.882 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 57 SER Chi-restraints excluded: chain A residue 117 VAL Chi-restraints excluded: chain E residue 118 THR Chi-restraints excluded: chain F residue 80 THR Chi-restraints excluded: chain F residue 95 ARG Chi-restraints excluded: chain G residue 54 SER Chi-restraints excluded: chain H residue 93 GLU Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 94 random chunks: chunk 60 optimal weight: 0.2980 chunk 72 optimal weight: 3.9990 chunk 67 optimal weight: 0.9980 chunk 19 optimal weight: 0.7980 chunk 44 optimal weight: 0.9980 chunk 28 optimal weight: 0.5980 chunk 32 optimal weight: 0.1980 chunk 58 optimal weight: 1.9990 chunk 14 optimal weight: 0.8980 chunk 25 optimal weight: 0.6980 chunk 51 optimal weight: 2.9990 overall best weight: 0.5180 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 25 ASN C 85 HIS E 68 GLN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3945 r_free = 0.3945 target = 0.169160 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 59)----------------| | r_work = 0.3544 r_free = 0.3544 target = 0.134065 restraints weight = 13570.797| |-----------------------------------------------------------------------------| r_work (start): 0.3521 rms_B_bonded: 0.82 r_work: 0.3370 rms_B_bonded: 2.49 restraints_weight: 0.5000 r_work: 0.3254 rms_B_bonded: 4.04 restraints_weight: 0.2500 r_work (final): 0.3254 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7989 moved from start: 0.4647 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.042 11786 Z= 0.173 Angle : 0.484 8.140 17012 Z= 0.280 Chirality : 0.032 0.131 1941 Planarity : 0.004 0.053 1262 Dihedral : 27.981 173.521 3618 Min Nonbonded Distance : 2.480 Molprobity Statistics. All-atom Clashscore : 3.69 Ramachandran Plot: Outliers : 0.28 % Allowed : 2.35 % Favored : 97.37 % Rotamer: Outliers : 2.63 % Allowed : 15.95 % Favored : 81.41 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.28 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.09 (0.29), residues: 722 helix: -0.10 (0.23), residues: 490 sheet: None (None), residues: 0 loop : -1.95 (0.31), residues: 232 Max deviation from planes: Type MaxDev MeanDev LineInFile HIS 0.004 0.001 HIS F 75 PHE 0.011 0.001 PHE F 61 TYR 0.015 0.001 TYR E 54 ARG 0.006 0.000 ARG F 35 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1444 Ramachandran restraints generated. 722 Oldfield, 0 Emsley, 722 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1444 Ramachandran restraints generated. 722 Oldfield, 0 Emsley, 722 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 146 residues out of total 608 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 16 poor density : 130 time to evaluate : 0.810 Fit side-chains REVERT: A 65 LEU cc_start: 0.9097 (OUTLIER) cc_final: 0.8819 (mt) REVERT: E 48 LEU cc_start: 0.8800 (OUTLIER) cc_final: 0.8402 (mp) REVERT: E 68 GLN cc_start: 0.8143 (tt0) cc_final: 0.7884 (mt0) REVERT: E 83 ARG cc_start: 0.8367 (OUTLIER) cc_final: 0.7652 (mtm180) REVERT: G 60 TYR cc_start: 0.8835 (t80) cc_final: 0.8610 (t80) outliers start: 16 outliers final: 4 residues processed: 138 average time/residue: 1.8417 time to fit residues: 267.5181 Evaluate side-chains 119 residues out of total 608 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 7 poor density : 112 time to evaluate : 0.861 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 57 SER Chi-restraints excluded: chain A residue 65 LEU Chi-restraints excluded: chain E residue 48 LEU Chi-restraints excluded: chain E residue 80 THR Chi-restraints excluded: chain E residue 83 ARG Chi-restraints excluded: chain E residue 118 THR Chi-restraints excluded: chain F residue 79 LYS Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 94 random chunks: chunk 24 optimal weight: 1.9990 chunk 93 optimal weight: 4.9990 chunk 83 optimal weight: 4.9990 chunk 34 optimal weight: 6.9990 chunk 85 optimal weight: 3.9990 chunk 17 optimal weight: 0.0770 chunk 54 optimal weight: 1.9990 chunk 56 optimal weight: 2.9990 chunk 23 optimal weight: 2.9990 chunk 88 optimal weight: 2.9990 chunk 53 optimal weight: 0.5980 overall best weight: 1.5344 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: E 68 GLN G 26 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3741 r_free = 0.3741 target = 0.151660 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 45)----------------| | r_work = 0.3287 r_free = 0.3287 target = 0.114846 restraints weight = 12962.398| |-----------------------------------------------------------------------------| r_work (start): 0.3242 rms_B_bonded: 0.82 r_work: 0.3075 rms_B_bonded: 2.42 restraints_weight: 0.5000 r_work: 0.2948 rms_B_bonded: 3.88 restraints_weight: 0.2500 r_work (final): 0.2948 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8303 moved from start: 0.6627 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.050 11786 Z= 0.328 Angle : 0.607 13.498 17012 Z= 0.339 Chirality : 0.038 0.135 1941 Planarity : 0.005 0.066 1262 Dihedral : 29.016 179.838 3618 Min Nonbonded Distance : 2.507 Molprobity Statistics. All-atom Clashscore : 4.69 Ramachandran Plot: Outliers : 0.28 % Allowed : 2.77 % Favored : 96.95 % Rotamer: Outliers : 3.95 % Allowed : 16.94 % Favored : 79.11 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.28 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.60 (0.30), residues: 722 helix: 0.16 (0.23), residues: 521 sheet: None (None), residues: 0 loop : -1.68 (0.34), residues: 201 Max deviation from planes: Type MaxDev MeanDev LineInFile HIS 0.008 0.001 HIS F 75 PHE 0.014 0.002 PHE F 61 TYR 0.015 0.002 TYR A 54 ARG 0.009 0.001 ARG H 86 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1444 Ramachandran restraints generated. 722 Oldfield, 0 Emsley, 722 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1444 Ramachandran restraints generated. 722 Oldfield, 0 Emsley, 722 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 163 residues out of total 608 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 24 poor density : 139 time to evaluate : 0.802 Fit side-chains REVERT: C 80 ARG cc_start: 0.8571 (mtm-85) cc_final: 0.8337 (mtm-85) REVERT: C 94 GLU cc_start: 0.7486 (tt0) cc_final: 0.7251 (mt-10) REVERT: E 48 LEU cc_start: 0.9056 (OUTLIER) cc_final: 0.8658 (mp) REVERT: E 52 ARG cc_start: 0.7383 (mtt-85) cc_final: 0.7107 (mtm110) REVERT: E 76 GLN cc_start: 0.8461 (tt0) cc_final: 0.8203 (tt0) REVERT: E 116 ARG cc_start: 0.8643 (OUTLIER) cc_final: 0.8241 (ttp-110) REVERT: E 133 GLU cc_start: 0.8289 (mt-10) cc_final: 0.8047 (mt-10) REVERT: G 37 LYS cc_start: 0.8842 (mtpp) cc_final: 0.8508 (mtpt) REVERT: G 60 TYR cc_start: 0.9042 (t80) cc_final: 0.8626 (t80) REVERT: G 91 ARG cc_start: 0.8894 (mmt90) cc_final: 0.8597 (mmt-90) REVERT: H 93 GLU cc_start: 0.8427 (OUTLIER) cc_final: 0.7819 (mp0) outliers start: 24 outliers final: 9 residues processed: 151 average time/residue: 1.8151 time to fit residues: 288.7742 Evaluate side-chains 129 residues out of total 608 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 12 poor density : 117 time to evaluate : 0.822 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 57 SER Chi-restraints excluded: chain A residue 65 LEU Chi-restraints excluded: chain A residue 117 VAL Chi-restraints excluded: chain E residue 48 LEU Chi-restraints excluded: chain E residue 56 LYS Chi-restraints excluded: chain E residue 80 THR Chi-restraints excluded: chain E residue 116 ARG Chi-restraints excluded: chain E residue 118 THR Chi-restraints excluded: chain F residue 79 LYS Chi-restraints excluded: chain G residue 40 THR Chi-restraints excluded: chain G residue 49 THR Chi-restraints excluded: chain H residue 93 GLU Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 94 random chunks: chunk 44 optimal weight: 0.6980 chunk 72 optimal weight: 3.9990 chunk 56 optimal weight: 1.9990 chunk 59 optimal weight: 2.9990 chunk 53 optimal weight: 2.9990 chunk 49 optimal weight: 0.8980 chunk 33 optimal weight: 0.8980 chunk 41 optimal weight: 0.7980 chunk 1 optimal weight: 2.9990 chunk 45 optimal weight: 0.6980 chunk 91 optimal weight: 3.9990 overall best weight: 0.7980 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 27 GLN C 33 HIS D 82 HIS E 68 GLN H 47 GLN H 84 ASN Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3749 r_free = 0.3749 target = 0.152161 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 55)----------------| | r_work = 0.3295 r_free = 0.3295 target = 0.115511 restraints weight = 12908.616| |-----------------------------------------------------------------------------| r_work (start): 0.3253 rms_B_bonded: 0.80 r_work: 0.3091 rms_B_bonded: 2.37 restraints_weight: 0.5000 r_work: 0.2963 rms_B_bonded: 3.83 restraints_weight: 0.2500 r_work (final): 0.2963 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8290 moved from start: 0.7042 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.045 11786 Z= 0.203 Angle : 0.506 12.607 17012 Z= 0.291 Chirality : 0.033 0.142 1941 Planarity : 0.004 0.036 1262 Dihedral : 28.872 176.020 3618 Min Nonbonded Distance : 2.479 Molprobity Statistics. All-atom Clashscore : 4.94 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.49 % Favored : 97.51 % Rotamer: Outliers : 2.80 % Allowed : 20.56 % Favored : 76.64 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.28 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.28 (0.31), residues: 722 helix: 0.84 (0.24), residues: 519 sheet: None (None), residues: 0 loop : -1.42 (0.35), residues: 203 Max deviation from planes: Type MaxDev MeanDev LineInFile HIS 0.007 0.001 HIS D 82 PHE 0.010 0.001 PHE E 78 TYR 0.009 0.001 TYR D 83 ARG 0.006 0.000 ARG H 86 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1444 Ramachandran restraints generated. 722 Oldfield, 0 Emsley, 722 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1444 Ramachandran restraints generated. 722 Oldfield, 0 Emsley, 722 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 144 residues out of total 608 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 17 poor density : 127 time to evaluate : 0.870 Fit side-chains REVERT: A 59 GLU cc_start: 0.8638 (OUTLIER) cc_final: 0.8315 (pm20) REVERT: A 65 LEU cc_start: 0.9136 (OUTLIER) cc_final: 0.8786 (mt) REVERT: B 79 LYS cc_start: 0.8728 (OUTLIER) cc_final: 0.8419 (mttm) REVERT: C 21 GLN cc_start: 0.8032 (tm-30) cc_final: 0.7667 (tt0) REVERT: C 80 ARG cc_start: 0.8608 (mtm-85) cc_final: 0.8360 (mtm-85) REVERT: C 94 GLU cc_start: 0.7470 (tt0) cc_final: 0.7222 (mt-10) REVERT: E 52 ARG cc_start: 0.7476 (mtt-85) cc_final: 0.7266 (mtm110) REVERT: E 76 GLN cc_start: 0.8494 (tt0) cc_final: 0.8202 (tt0) outliers start: 17 outliers final: 12 residues processed: 137 average time/residue: 1.8066 time to fit residues: 261.2807 Evaluate side-chains 131 residues out of total 608 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 15 poor density : 116 time to evaluate : 0.912 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 57 SER Chi-restraints excluded: chain A residue 59 GLU Chi-restraints excluded: chain A residue 65 LEU Chi-restraints excluded: chain A residue 117 VAL Chi-restraints excluded: chain B residue 79 LYS Chi-restraints excluded: chain C residue 17 VAL Chi-restraints excluded: chain D residue 56 SER Chi-restraints excluded: chain D residue 87 SER Chi-restraints excluded: chain E residue 80 THR Chi-restraints excluded: chain E residue 105 GLU Chi-restraints excluded: chain E residue 118 THR Chi-restraints excluded: chain F residue 79 LYS Chi-restraints excluded: chain G residue 40 THR Chi-restraints excluded: chain G residue 49 THR Chi-restraints excluded: chain H residue 112 SER Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 94 random chunks: chunk 33 optimal weight: 0.6980 chunk 53 optimal weight: 0.0050 chunk 3 optimal weight: 1.9990 chunk 51 optimal weight: 3.9990 chunk 86 optimal weight: 3.9990 chunk 69 optimal weight: 1.9990 chunk 63 optimal weight: 1.9990 chunk 26 optimal weight: 0.9980 chunk 84 optimal weight: 4.9990 chunk 60 optimal weight: 0.9990 chunk 16 optimal weight: 4.9990 overall best weight: 0.9398 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: D 82 HIS E 68 GLN F 75 HIS ** H 47 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** H 82 HIS H 84 ASN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3701 r_free = 0.3701 target = 0.148083 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 61)----------------| | r_work = 0.3236 r_free = 0.3236 target = 0.111070 restraints weight = 12989.753| |-----------------------------------------------------------------------------| r_work (start): 0.3208 rms_B_bonded: 0.78 r_work: 0.3051 rms_B_bonded: 2.27 restraints_weight: 0.5000 r_work: 0.2926 rms_B_bonded: 3.66 restraints_weight: 0.2500 r_work (final): 0.2926 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8326 moved from start: 0.7561 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.049 11786 Z= 0.234 Angle : 0.539 14.426 17012 Z= 0.308 Chirality : 0.034 0.159 1941 Planarity : 0.004 0.038 1262 Dihedral : 29.211 170.725 3618 Min Nonbonded Distance : 2.451 Molprobity Statistics. All-atom Clashscore : 4.59 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.46 % Favored : 96.54 % Rotamer: Outliers : 4.11 % Allowed : 19.08 % Favored : 76.81 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.28 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.62 (0.31), residues: 722 helix: 1.14 (0.24), residues: 522 sheet: None (None), residues: 0 loop : -1.48 (0.35), residues: 200 Max deviation from planes: Type MaxDev MeanDev LineInFile HIS 0.006 0.001 HIS D 82 PHE 0.011 0.002 PHE E 78 TYR 0.010 0.001 TYR H 121 ARG 0.008 0.000 ARG H 86 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1444 Ramachandran restraints generated. 722 Oldfield, 0 Emsley, 722 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1444 Ramachandran restraints generated. 722 Oldfield, 0 Emsley, 722 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 152 residues out of total 608 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 25 poor density : 127 time to evaluate : 0.826 Fit side-chains REVERT: A 79 LYS cc_start: 0.7629 (tttm) cc_final: 0.7326 (tttm) REVERT: B 79 LYS cc_start: 0.8753 (OUTLIER) cc_final: 0.8304 (mttm) REVERT: C 21 GLN cc_start: 0.8055 (tm-30) cc_final: 0.7703 (tt0) REVERT: C 80 ARG cc_start: 0.8641 (mtm-85) cc_final: 0.8372 (mtm-85) REVERT: C 94 GLU cc_start: 0.7577 (tt0) cc_final: 0.7331 (mt-10) REVERT: D 33 ARG cc_start: 0.5654 (ttm170) cc_final: 0.5122 (ttt180) REVERT: E 52 ARG cc_start: 0.7624 (mtt-85) cc_final: 0.7354 (mtm110) REVERT: E 76 GLN cc_start: 0.8483 (tt0) cc_final: 0.8191 (tt0) REVERT: E 116 ARG cc_start: 0.8688 (OUTLIER) cc_final: 0.8229 (ttp-170) REVERT: G 60 TYR cc_start: 0.9078 (t80) cc_final: 0.8864 (t80) outliers start: 25 outliers final: 16 residues processed: 141 average time/residue: 1.7880 time to fit residues: 266.0158 Evaluate side-chains 140 residues out of total 608 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 18 poor density : 122 time to evaluate : 0.900 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 57 SER Chi-restraints excluded: chain A residue 65 LEU Chi-restraints excluded: chain A residue 117 VAL Chi-restraints excluded: chain B residue 79 LYS Chi-restraints excluded: chain C residue 17 VAL Chi-restraints excluded: chain C residue 38 SER Chi-restraints excluded: chain D residue 87 SER Chi-restraints excluded: chain E residue 80 THR Chi-restraints excluded: chain E residue 116 ARG Chi-restraints excluded: chain E residue 118 THR Chi-restraints excluded: chain F residue 79 LYS Chi-restraints excluded: chain G residue 40 THR Chi-restraints excluded: chain G residue 49 THR Chi-restraints excluded: chain H residue 48 VAL Chi-restraints excluded: chain H residue 56 SER Chi-restraints excluded: chain H residue 78 SER Chi-restraints excluded: chain H residue 112 SER Chi-restraints excluded: chain H residue 122 THR Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 94 random chunks: chunk 91 optimal weight: 3.9990 chunk 33 optimal weight: 0.7980 chunk 53 optimal weight: 0.9980 chunk 19 optimal weight: 0.8980 chunk 35 optimal weight: 0.0980 chunk 48 optimal weight: 2.9990 chunk 39 optimal weight: 1.9990 chunk 81 optimal weight: 4.9990 chunk 36 optimal weight: 0.6980 chunk 72 optimal weight: 3.9990 chunk 83 optimal weight: 4.9990 overall best weight: 0.6980 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 27 GLN D 82 HIS E 68 GLN H 47 GLN H 82 HIS H 84 ASN Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3713 r_free = 0.3713 target = 0.149166 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 46)----------------| | r_work = 0.3254 r_free = 0.3254 target = 0.112455 restraints weight = 13065.889| |-----------------------------------------------------------------------------| r_work (start): 0.3181 rms_B_bonded: 0.79 r_work: 0.3021 rms_B_bonded: 2.26 restraints_weight: 0.5000 r_work: 0.2896 rms_B_bonded: 3.63 restraints_weight: 0.2500 r_work (final): 0.2896 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8307 moved from start: 0.7629 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.054 11786 Z= 0.200 Angle : 0.518 14.406 17012 Z= 0.296 Chirality : 0.032 0.156 1941 Planarity : 0.004 0.036 1262 Dihedral : 29.082 170.046 3618 Min Nonbonded Distance : 2.486 Molprobity Statistics. All-atom Clashscore : 4.69 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.77 % Favored : 97.23 % Rotamer: Outliers : 4.11 % Allowed : 19.41 % Favored : 76.48 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.28 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.07 (0.32), residues: 722 helix: 1.47 (0.24), residues: 522 sheet: None (None), residues: 0 loop : -1.32 (0.36), residues: 200 Max deviation from planes: Type MaxDev MeanDev LineInFile HIS 0.008 0.001 HIS D 82 PHE 0.007 0.001 PHE E 78 TYR 0.009 0.001 TYR H 121 ARG 0.003 0.000 ARG C 80 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1444 Ramachandran restraints generated. 722 Oldfield, 0 Emsley, 722 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1444 Ramachandran restraints generated. 722 Oldfield, 0 Emsley, 722 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 148 residues out of total 608 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 25 poor density : 123 time to evaluate : 0.816 Fit side-chains REVERT: A 59 GLU cc_start: 0.8552 (OUTLIER) cc_final: 0.8199 (pm20) REVERT: A 79 LYS cc_start: 0.7634 (tttm) cc_final: 0.7326 (tttm) REVERT: C 21 GLN cc_start: 0.8052 (tm-30) cc_final: 0.7687 (tt0) REVERT: C 94 GLU cc_start: 0.7531 (tt0) cc_final: 0.7293 (mt-10) REVERT: D 33 ARG cc_start: 0.5671 (ttm170) cc_final: 0.5129 (ttt180) REVERT: E 48 LEU cc_start: 0.9036 (OUTLIER) cc_final: 0.8610 (mp) REVERT: E 52 ARG cc_start: 0.7642 (mtt-85) cc_final: 0.7308 (mtm110) REVERT: E 76 GLN cc_start: 0.8496 (tt0) cc_final: 0.8201 (tt0) REVERT: E 116 ARG cc_start: 0.8687 (OUTLIER) cc_final: 0.8177 (ttp-170) REVERT: G 60 TYR cc_start: 0.9056 (t80) cc_final: 0.8825 (t80) REVERT: H 93 GLU cc_start: 0.8417 (OUTLIER) cc_final: 0.7804 (mp0) outliers start: 25 outliers final: 15 residues processed: 138 average time/residue: 1.8135 time to fit residues: 263.7203 Evaluate side-chains 140 residues out of total 608 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 19 poor density : 121 time to evaluate : 0.900 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 57 SER Chi-restraints excluded: chain A residue 59 GLU Chi-restraints excluded: chain A residue 65 LEU Chi-restraints excluded: chain A residue 117 VAL Chi-restraints excluded: chain C residue 17 VAL Chi-restraints excluded: chain C residue 25 LEU Chi-restraints excluded: chain C residue 38 SER Chi-restraints excluded: chain D residue 87 SER Chi-restraints excluded: chain E residue 48 LEU Chi-restraints excluded: chain E residue 80 THR Chi-restraints excluded: chain E residue 105 GLU Chi-restraints excluded: chain E residue 116 ARG Chi-restraints excluded: chain E residue 118 THR Chi-restraints excluded: chain F residue 79 LYS Chi-restraints excluded: chain G residue 40 THR Chi-restraints excluded: chain G residue 49 THR Chi-restraints excluded: chain H residue 78 SER Chi-restraints excluded: chain H residue 93 GLU Chi-restraints excluded: chain H residue 112 SER Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 94 random chunks: chunk 28 optimal weight: 2.9990 chunk 44 optimal weight: 0.8980 chunk 48 optimal weight: 0.6980 chunk 31 optimal weight: 0.7980 chunk 66 optimal weight: 4.9990 chunk 83 optimal weight: 4.9990 chunk 39 optimal weight: 0.5980 chunk 63 optimal weight: 2.9990 chunk 17 optimal weight: 2.9990 chunk 35 optimal weight: 2.9990 chunk 0 optimal weight: 5.9990 overall best weight: 1.1982 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: D 82 HIS E 68 GLN H 47 GLN H 82 HIS H 84 ASN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3674 r_free = 0.3674 target = 0.146185 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 45)----------------| | r_work = 0.3205 r_free = 0.3205 target = 0.109210 restraints weight = 12961.000| |-----------------------------------------------------------------------------| r_work (start): 0.3137 rms_B_bonded: 0.80 r_work: 0.2969 rms_B_bonded: 2.29 restraints_weight: 0.5000 r_work: 0.2840 rms_B_bonded: 3.66 restraints_weight: 0.2500 r_work (final): 0.2840 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8362 moved from start: 0.8009 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.053 11786 Z= 0.270 Angle : 0.569 15.536 17012 Z= 0.322 Chirality : 0.035 0.142 1941 Planarity : 0.004 0.060 1262 Dihedral : 29.425 165.040 3618 Min Nonbonded Distance : 2.535 Molprobity Statistics. All-atom Clashscore : 4.24 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.60 % Favored : 96.40 % Rotamer: Outliers : 4.28 % Allowed : 18.59 % Favored : 77.14 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.28 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.02 (0.32), residues: 722 helix: 1.42 (0.24), residues: 523 sheet: None (None), residues: 0 loop : -1.32 (0.37), residues: 199 Max deviation from planes: Type MaxDev MeanDev LineInFile HIS 0.007 0.001 HIS H 82 PHE 0.010 0.002 PHE E 78 TYR 0.010 0.001 TYR A 54 ARG 0.002 0.000 ARG B 45 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1444 Ramachandran restraints generated. 722 Oldfield, 0 Emsley, 722 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1444 Ramachandran restraints generated. 722 Oldfield, 0 Emsley, 722 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 151 residues out of total 608 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 26 poor density : 125 time to evaluate : 0.872 Fit side-chains REVERT: C 21 GLN cc_start: 0.8079 (tm-30) cc_final: 0.7715 (tt0) REVERT: C 94 GLU cc_start: 0.7609 (tt0) cc_final: 0.7375 (mt-10) REVERT: E 52 ARG cc_start: 0.7734 (mtt-85) cc_final: 0.7403 (mtm110) REVERT: E 76 GLN cc_start: 0.8511 (tt0) cc_final: 0.8183 (tt0) REVERT: E 116 ARG cc_start: 0.8748 (OUTLIER) cc_final: 0.8297 (ttp-170) REVERT: G 37 LYS cc_start: 0.8748 (mtpp) cc_final: 0.8433 (mtpt) REVERT: G 60 TYR cc_start: 0.9085 (t80) cc_final: 0.8873 (t80) REVERT: H 93 GLU cc_start: 0.8446 (OUTLIER) cc_final: 0.7864 (mp0) outliers start: 26 outliers final: 20 residues processed: 137 average time/residue: 1.7826 time to fit residues: 257.7190 Evaluate side-chains 144 residues out of total 608 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 22 poor density : 122 time to evaluate : 0.952 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 57 SER Chi-restraints excluded: chain A residue 65 LEU Chi-restraints excluded: chain A residue 86 SER Chi-restraints excluded: chain A residue 117 VAL Chi-restraints excluded: chain C residue 17 VAL Chi-restraints excluded: chain C residue 38 SER Chi-restraints excluded: chain D residue 56 SER Chi-restraints excluded: chain D residue 87 SER Chi-restraints excluded: chain E residue 80 THR Chi-restraints excluded: chain E residue 105 GLU Chi-restraints excluded: chain E residue 116 ARG Chi-restraints excluded: chain E residue 118 THR Chi-restraints excluded: chain E residue 129 ARG Chi-restraints excluded: chain F residue 79 LYS Chi-restraints excluded: chain G residue 40 THR Chi-restraints excluded: chain G residue 49 THR Chi-restraints excluded: chain H residue 48 VAL Chi-restraints excluded: chain H residue 56 SER Chi-restraints excluded: chain H residue 78 SER Chi-restraints excluded: chain H residue 93 GLU Chi-restraints excluded: chain H residue 112 SER Chi-restraints excluded: chain H residue 122 THR Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 94 random chunks: chunk 2 optimal weight: 0.5980 chunk 66 optimal weight: 0.6980 chunk 18 optimal weight: 4.9990 chunk 65 optimal weight: 0.9990 chunk 67 optimal weight: 2.9990 chunk 90 optimal weight: 3.9990 chunk 31 optimal weight: 0.3980 chunk 62 optimal weight: 0.0270 chunk 60 optimal weight: 2.9990 chunk 4 optimal weight: 0.9980 chunk 49 optimal weight: 0.7980 overall best weight: 0.5038 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: D 82 HIS E 68 GLN H 47 GLN H 82 HIS H 84 ASN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3697 r_free = 0.3697 target = 0.147505 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 46)----------------| | r_work = 0.3224 r_free = 0.3224 target = 0.109970 restraints weight = 13191.144| |-----------------------------------------------------------------------------| r_work (start): 0.3192 rms_B_bonded: 0.85 r_work: 0.3028 rms_B_bonded: 2.40 restraints_weight: 0.5000 r_work: 0.2900 rms_B_bonded: 3.85 restraints_weight: 0.2500 r_work (final): 0.2900 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8337 moved from start: 0.8002 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.047 11786 Z= 0.179 Angle : 0.525 14.485 17012 Z= 0.302 Chirality : 0.032 0.140 1941 Planarity : 0.003 0.035 1262 Dihedral : 29.192 163.906 3618 Min Nonbonded Distance : 2.495 Molprobity Statistics. All-atom Clashscore : 4.99 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.49 % Favored : 97.51 % Rotamer: Outliers : 1.97 % Allowed : 22.20 % Favored : 75.82 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.28 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.43 (0.32), residues: 722 helix: 1.73 (0.24), residues: 523 sheet: None (None), residues: 0 loop : -1.18 (0.38), residues: 199 Max deviation from planes: Type MaxDev MeanDev LineInFile HIS 0.009 0.001 HIS D 82 PHE 0.005 0.001 PHE F 61 TYR 0.009 0.001 TYR H 121 ARG 0.003 0.000 ARG C 80 *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1444 Ramachandran restraints generated. 722 Oldfield, 0 Emsley, 722 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1444 Ramachandran restraints generated. 722 Oldfield, 0 Emsley, 722 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 138 residues out of total 608 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 12 poor density : 126 time to evaluate : 0.856 Fit side-chains REVERT: A 65 LEU cc_start: 0.9112 (OUTLIER) cc_final: 0.8889 (mt) REVERT: A 79 LYS cc_start: 0.7618 (tttm) cc_final: 0.7323 (tttm) REVERT: C 21 GLN cc_start: 0.8140 (tm-30) cc_final: 0.7706 (tt0) REVERT: C 94 GLU cc_start: 0.7496 (tt0) cc_final: 0.7266 (mt-10) REVERT: E 52 ARG cc_start: 0.7713 (mtt-85) cc_final: 0.7422 (mtm110) REVERT: E 76 GLN cc_start: 0.8489 (tt0) cc_final: 0.8169 (tt0) REVERT: G 37 LYS cc_start: 0.8761 (mtpp) cc_final: 0.8459 (mtpt) REVERT: H 93 GLU cc_start: 0.8436 (OUTLIER) cc_final: 0.7819 (mp0) outliers start: 12 outliers final: 6 residues processed: 129 average time/residue: 1.8510 time to fit residues: 252.0903 Evaluate side-chains 131 residues out of total 608 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 8 poor density : 123 time to evaluate : 0.887 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 65 LEU Chi-restraints excluded: chain C residue 17 VAL Chi-restraints excluded: chain D residue 87 SER Chi-restraints excluded: chain E residue 105 GLU Chi-restraints excluded: chain E residue 118 THR Chi-restraints excluded: chain F residue 79 LYS Chi-restraints excluded: chain G residue 49 THR Chi-restraints excluded: chain H residue 93 GLU Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 94 random chunks: chunk 33 optimal weight: 0.7980 chunk 39 optimal weight: 0.7980 chunk 70 optimal weight: 7.9990 chunk 52 optimal weight: 1.9990 chunk 35 optimal weight: 0.7980 chunk 4 optimal weight: 2.9990 chunk 1 optimal weight: 0.8980 chunk 59 optimal weight: 1.9990 chunk 69 optimal weight: 0.5980 chunk 8 optimal weight: 0.9990 chunk 9 optimal weight: 3.9990 overall best weight: 0.7780 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: D 82 HIS E 68 GLN H 47 GLN H 82 HIS H 84 ASN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3683 r_free = 0.3683 target = 0.146368 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 58)----------------| | r_work = 0.3211 r_free = 0.3211 target = 0.109027 restraints weight = 13145.374| |-----------------------------------------------------------------------------| r_work (start): 0.3185 rms_B_bonded: 0.80 r_work: 0.3021 rms_B_bonded: 2.33 restraints_weight: 0.5000 r_work: 0.2895 rms_B_bonded: 3.71 restraints_weight: 0.2500 r_work (final): 0.2895 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8341 moved from start: 0.8040 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.064 11786 Z= 0.213 Angle : 0.534 14.595 17012 Z= 0.304 Chirality : 0.033 0.154 1941 Planarity : 0.004 0.059 1262 Dihedral : 29.235 165.165 3618 Min Nonbonded Distance : 2.517 Molprobity Statistics. All-atom Clashscore : 5.19 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.05 % Favored : 96.95 % Rotamer: Outliers : 1.97 % Allowed : 21.71 % Favored : 76.32 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.28 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.48 (0.32), residues: 722 helix: 1.76 (0.24), residues: 523 sheet: None (None), residues: 0 loop : -1.15 (0.38), residues: 199 Max deviation from planes: Type MaxDev MeanDev LineInFile HIS 0.007 0.001 HIS H 82 PHE 0.007 0.001 PHE E 84 TYR 0.009 0.001 TYR E 54 ARG 0.006 0.000 ARG F 35 ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1444 Ramachandran restraints generated. 722 Oldfield, 0 Emsley, 722 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1444 Ramachandran restraints generated. 722 Oldfield, 0 Emsley, 722 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 136 residues out of total 608 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 12 poor density : 124 time to evaluate : 0.807 Fit side-chains REVERT: A 79 LYS cc_start: 0.7679 (tttm) cc_final: 0.7387 (tttm) REVERT: A 120 MET cc_start: 0.8472 (OUTLIER) cc_final: 0.7982 (mtm) REVERT: C 21 GLN cc_start: 0.8130 (tm-30) cc_final: 0.7704 (tt0) REVERT: C 94 GLU cc_start: 0.7570 (tt0) cc_final: 0.7345 (mt-10) REVERT: E 52 ARG cc_start: 0.7706 (mtt-85) cc_final: 0.7408 (mtm110) REVERT: E 76 GLN cc_start: 0.8502 (tt0) cc_final: 0.8207 (tt0) REVERT: E 116 ARG cc_start: 0.8695 (OUTLIER) cc_final: 0.8054 (ttp-170) REVERT: G 37 LYS cc_start: 0.8745 (mtpp) cc_final: 0.8438 (mtpt) REVERT: H 93 GLU cc_start: 0.8445 (OUTLIER) cc_final: 0.7858 (mp0) outliers start: 12 outliers final: 8 residues processed: 129 average time/residue: 1.8253 time to fit residues: 248.0452 Evaluate side-chains 134 residues out of total 608 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 11 poor density : 123 time to evaluate : 0.819 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 65 LEU Chi-restraints excluded: chain A residue 120 MET Chi-restraints excluded: chain C residue 17 VAL Chi-restraints excluded: chain D residue 87 SER Chi-restraints excluded: chain E residue 116 ARG Chi-restraints excluded: chain E residue 118 THR Chi-restraints excluded: chain E residue 129 ARG Chi-restraints excluded: chain F residue 63 GLU Chi-restraints excluded: chain F residue 79 LYS Chi-restraints excluded: chain G residue 49 THR Chi-restraints excluded: chain H residue 93 GLU Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 94 random chunks: chunk 69 optimal weight: 1.9990 chunk 43 optimal weight: 2.9990 chunk 63 optimal weight: 0.9990 chunk 61 optimal weight: 2.9990 chunk 70 optimal weight: 7.9990 chunk 66 optimal weight: 3.9990 chunk 47 optimal weight: 0.6980 chunk 26 optimal weight: 0.2980 chunk 17 optimal weight: 3.9990 chunk 76 optimal weight: 3.9990 chunk 77 optimal weight: 3.9990 overall best weight: 1.3986 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: D 82 HIS E 68 GLN H 47 GLN H 82 HIS H 84 ASN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3658 r_free = 0.3658 target = 0.144617 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 55)----------------| | r_work = 0.3185 r_free = 0.3185 target = 0.107306 restraints weight = 13190.038| |-----------------------------------------------------------------------------| r_work (start): 0.3148 rms_B_bonded: 0.81 r_work: 0.2984 rms_B_bonded: 2.30 restraints_weight: 0.5000 r_work: 0.2856 rms_B_bonded: 3.67 restraints_weight: 0.2500 r_work (final): 0.2856 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8381 moved from start: 0.8252 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.073 11786 Z= 0.295 Angle : 0.585 15.407 17012 Z= 0.330 Chirality : 0.036 0.140 1941 Planarity : 0.005 0.075 1262 Dihedral : 29.524 167.238 3618 Min Nonbonded Distance : 2.522 Molprobity Statistics. All-atom Clashscore : 5.14 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.46 % Favored : 96.54 % Rotamer: Outliers : 2.30 % Allowed : 21.88 % Favored : 75.82 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.28 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.23 (0.32), residues: 722 helix: 1.56 (0.24), residues: 523 sheet: None (None), residues: 0 loop : -1.18 (0.38), residues: 199 Max deviation from planes: Type MaxDev MeanDev LineInFile HIS 0.009 0.001 HIS H 82 PHE 0.010 0.002 PHE E 78 TYR 0.013 0.001 TYR G 60 ARG 0.006 0.000 ARG F 35 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 8025.21 seconds wall clock time: 142 minutes 3.25 seconds (8523.25 seconds total)